File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/007ebcce901c87b84e196c8bcec86a/.command.sh
Size
940 bytes
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS (germline_control_2)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
gatk --java-options "-Xmx3276M -XX:-UsePerfData" \
    MergeVcfs \
    --INPUT germline_control_2.haplotyper.chr14_64122012-64122133.bed.unfiltered.vcf.gz --INPUT germline_control_2.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz --INPUT germline_control_2.haplotyper.chr1_69091-70008.bed.unfiltered.vcf.gz --INPUT germline_control_2.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz --INPUT germline_control_2.haplotyper.chr8_93795409-93795507.bed.unfiltered.vcf.gz \
    --OUTPUT germline_control_2.haplotyper.unfiltered.vcf.gz \
    --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict \
    --TMP_DIR . \


cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS":
    gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//')
END_VERSIONS